[Bio-linux-dev] [Bio-Linux] How to Install all packages on Ubuntu?

Jasmine Lognnes princess.jasmine.lognnes at gmail.com
Fri Feb 14 07:51:30 EST 2014


Dear Jan,

The script added those for me, but looking at the repos in a browser,
I can't see the bio-linux-assembly-conversion-tools in any of the
repos. apt-cache search bio-linux | assembly doesn't give any hits
either.

However I see the package installed on the liveUSB stick. Have it been
made from another repo?

Hugs,
Jasmine =)







On 14 February 2014 13:38, Troesemeier, Jan-Hendrik
<Jan-Hendrik.Troesemeier at pei.de> wrote:
> Dear Jasmine,
>
> have you added the biolinux repositories (e.g. explained in http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/package-repository )? Afaik the missing package is a biolinux-repo only one.
>
> Cheers,
> jan
>
> -----Ursprüngliche Nachricht-----
> Von: Jasmine Lognnes [mailto:princess.jasmine.lognnes at gmail.com]
> Gesendet: Freitag, 14. Februar 2014 11:29
> An: Bio-Linux help and discussion
> Cc: Bio-Linux technical discussion
> Betreff: Re: [Bio-linux-dev] [Bio-Linux] How to Install all packages on Ubuntu?
>
> Dear Tony,
>
> That is good news. I have now tried it on a fresh Ubuntu 12.04 64bit, and it exits with pasted in at the bottom. What can you gather from this?
>
> Hugs,
> Jasmine =)
>
>
>
> The following NEW packages will be installed:
>   bio-linux-artemis
> 0 upgraded, 1 newly installed, 0 to remove and 14 not upgraded.
> Need to get 11.8 MB of archives.
> After this operation, 47.7 MB of additional disk space will be used.
> Get:1 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux bio-linux-artemis all 15.1.1-1 [11.8 MB] Fetched 11.8 MB in 2s (5,111 kB/s) Selecting previously unselected package bio-linux-artemis.
> (Reading database ... 162928 files and directories currently installed.) Unpacking bio-linux-artemis (from .../bio-linux-artemis_15.1.1-1_all.deb) ...
> Processing triggers for bamfdaemon ...
> Rebuilding /usr/share/applications/bamf.index...
> Processing triggers for desktop-file-utils ...
> Processing triggers for gnome-menus ...
> Setting up bio-linux-artemis (15.1.1-1) ...
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> E: Unable to locate package bio-linux-assembly-conversion-tools
> Not all packages installed properly - exiting.
>
>
>
>
>
>
>
> On 12 February 2014 16:32, Tony Travis <tony.travis at abdn.ac.uk> wrote:
>>
>> On 12/02/14 15:03, Jasmine Lognnes wrote:
>> > Dear Tim,
>> >
>> > That's a very impressive script. Wow!
>> >
>> > By going through the script I have cherry picked what looks like to
>> > be needed on a plain Ubuntu 12.04 64bit. I have attached it as a script.
>> > Can you verify that it is the correct procedure?
>> >
>> > On the liveUSB I did
>> >
>> > grep "^Packages: bio-linux" /var/lib/dpkg/status | awk '{print $2}'
>> >
>> > and got the attached list of packages. On a successful installation,
>> > should I end up these exact packages?
>>
>> Hi, Jasmine.
>>
>> I've used Tim's 6>7 script to install Bio-Linux on pre-existing Ubuntu
>> 12.04 LTS systems without any problems. You don't need to grep things
>> out like you did. Just run the script in its entirety and please email
>> any bug reports to the bio-linux-dev list.
>>
>> HTH,
>>
>>   Tony.
>>
>> --
>> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
>> Environmental Sciences, Cruickshank Building, St. Machar Drive,
>> Aberdeen
>> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
>> http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
>> The University of Aberdeen is a charity registered in Scotland, No SC013683.
>> _______________________________________________
>> Bio-Linux mailing list
>> Bio-Linux at nebclists.nerc.ac.uk
>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> _______________________________________________
> Bio-Linux-dev mailing list
> Bio-Linux-dev at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> _______________________________________________
> Bio-Linux-dev mailing list
> Bio-Linux-dev at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev



More information about the Bio-linux-devel mailing list